Topoisomerase I (Top1) is an enzyme that is believed to relax supercoiled DNA. Relaxed DNA is reported to be required for many cellular processes such as DNA replication, transcription, and repair. Top1 is believed to relax DNA through a cycle of cleavage and religation steps involving the active site residue Tyr723. This residue is believed to attack the phosphodiester backbone, breaking the single strand and forming a covalent “cleavage complex” in which the unbroken strand undergoes “controlled rotation” and relaxes the DNA. After relaxation, the scissile strand is believed to be religated and the enzyme is released. As inhibition of Top1 is believed to be capable of leading to cell death, several Top1 inhibitors have been reportedly developed as a targeted approach for anti-cancer therapy. Camptothecin (1) and its clinically used analogues, topotecan (2) and irinotecan (3), were reported to inhibit Top1 activity by intercalating into the cleavage complex and preventing the religation step of the catalytic cycle. As a result, it is believed that advancing replication forks collide with the cleavage complex, resulting in double-stranded DNA breaks and apoptosis. Compounds that inhibit the religation reaction are commonly known as “Top1 poisons”.

Although these inhibitors are reported to possess potent antitumor activity, issues regarding solubility and bioactivity, dose-limiting toxicity, and importantly, the instability of the hydroxy lactone and associated pharmacokinetic liabilities, have reportedly led to the development of therapeutic alternatives. A COMPARE analysis[Paull, K. D. et al., J. Natl. Cancer Inst. 1989, 81, 1088-1092] performed on the cytotoxicity profile of synthetic indenoisoquinoline 4 has been reported as showing many similarities to the cytotoxicity profile of camptothecin, indicating that compound 4 may exert its action through inhibition of Top1. [Pommier, Y. and Cushman, M., Mol. Cancer Ther. 2009, 8, 1008-1014.] Indeed, indenoisoquinolines such as 4 are believed to inhibit the religation reaction by an intercalative mechanism like camptothecin. Additionally, indenoisoquinolines are believed to be chemically stable, and many compounds in this class are believed to possess high antiproliferative activity.
It has been discovered herein that indenoisoquinolines can be modified to include branched or cyclic alkanols, or a hydroxy prodrugs thereof, and that the modified indenoisoquinolines are potent modulators of Top1 activity. Without being bound by theory, it is believed herein that indenoisoquinolines described herein form additional hydrogen bonds with residues available in the ternary complex. A comparison of crystal structures of Top1 ternary complexes is believed to reveal that branched or cyclic alkanols extend further out into the DNA major groove region. The aromatic core of the compounds appears to face Arg364 (with which they likely interact). The side chain appears to sit in close proximity to Asn352 and occupy similar spatial areas, where, accounting for flexibility, it is believed it may hydrogen bond with this residue, water, or flanking base pairs.
In one embodiment, described herein are the design, synthesis, and evaluation of indenoisoquinolines containing an N-branched or cyclic alkanol substituent, or a hydroxy prodrug thereof. In another illustrative embodiment, the indenoisoquinolines herein include compounds substituted with amines derived from aldohexoses and aldopentoses. In another illustrative embodiment, the indenoisoquinolines herein include compounds bearing shorter chiral side chains.
In another embodiment, described herein are compounds and compositions comprising series of alcohol, diol, and carbohydrate-substituted indenoisoquinolines. In another embodiment, described herein are the syntheses of these series of alcohol, diol, and carbohydrate-substituted indenoisoquinolines. In another embodiment, described herein are biological evaluations of these series of alcohol, diol, and carbohydrate-substituted indenoisoquinolines. In another embodiment, compounds described herein, including aldopentose and aldohexose-derived indenoisoquinolines, show activity across a panel of cancer cell lines. In another embodiment, compounds described herein show potent Top1 inhibitory activity when compared to camptothecin. In another embodiment, several of the compounds herein display potent Top1 poisoning and antiproliferative activities.
In another embodiment, indenoisoquinolines substituted with three-carbon alcohols and diols are described herein. In another embodiment, these three-carbon alcohol and diol-derived indenoisoquinolines appear to demonstrate activity across a panel of cancer cell lines. In another embodiment, several of these compounds appear to display potent Top1 inhibitory activity.
In one aspect of the Top1 inhibitory activity of the compounds herein, a stereochemical effect is observed.
In another embodiment, it is demonstrated herein that the activity of the indenoisoquinolines herein can be increased by ring substitution and by replacement of a primary alcohol with an amino group.
In another embodiment, pharmaceutical compositions containing one or more of the compounds are also described herein. In one aspect, the compositions include a therapeutically effective amount of the one or more compounds for treating a patient with cancer. It is to be understood that the compositions may include other components and/or ingredients, including, but not limited to, other therapeutically active compounds, and/or one or more carriers, diluents, excipients, and the like. In another embodiment, methods for using the compounds and pharmaceutical compositions for treating patients with cancer are also described herein. In one aspect, the methods include the step of administering one or more of the compounds and/or compositions described herein to a patient with cancer. In another aspect, the methods include administering a therapeutically effective amount of the one or more compounds and/or compositions described herein for treating patients with cancer. In another embodiment, uses of the compounds and compositions in the manufacture of a medicament for treating patients with cancer are also described herein. In one aspect, the medicaments include a therapeutically effective amount of the one or more compounds and/or compositions for treating a patient with cancer.